GSM6042012: ChIP-seq GC4270 K562 control CTCF rep2; Homo sapiens; ChIP-Seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
TFs and others
Antigen
CTCF
Cell type
Cell type Class
Blood
Cell type
K-562
Primary Tissue
Blood
Tissue Diagnosis
Leukemia Chronic Myelogenous
Attributes by original data submitter
Sample
source_name
K562
cell line
K562
tissue
K562
genotype/variation
shRNA control
antibody
CTCF antibody
Sequenced DNA Library
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For Hi-TrAC and Hi-C, genomic DNA was purified by Phenol-Chloroform extraction. RNA was extracted with QIAzol lysis reagent (QIAGEN) and RNeasy mini kit (QIAGEN). For ChIP-seq and ATAC-seq, genomic DNA was purified with QIAGEN MinElute Reaction Cleanup Kit. For Hi-TrAC, repair DNA gaps with T4 DNA polymerase. Remove free bridging linker by AMPure XP beads. Then, Digest purified DNA with restriction enzymes MluCI/NlaIII, and enrich biotin-labeled DNA fragments with streptavidin beads. Perform adapter ligation on beads. After washing the beads, run PCR with illumina multiplexing indexed primers. For RNA-seq, libraries were constructed following Smart-seq2 protocol (Picelli et al., 2014). For ChIP-seq, DNA was purified, then end-repaired using End-It DNA End-Repair kit (Epicentre). A-tailing was performed with Klenow Fragment (3'->5' exo-) with the presence of dATP. Universal adapters were then ligated. The libraries were then amplified by PCR using indexed primers. For ATAC-seq, purified genomic DNA was amplified by PCR with indexed primers to construct the libraries. For Hi-C, purified genomic DNA was treated with T4 DNA polymerase to remove biotin labels at DNA ends. Fragment the DNA by sonication to 300-500 bp. Fragmentated DNA was end-repaired, followed with A-tailing. Biotin labeled DNA was enriched with MyOne Streptavidin C1 beads (Invitrogen). PCR adapters were then ligated to the enriched DNA on beads. Perform PCR with indexed primers to amplify the libraries.